From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sun Oct 25 2020 - 20:34:15 CDT

Ok, that's what I thought. No worries, I will try that command and see if I can get something to work.

Dr. Kelly L. McGuire

PhD Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Ren Hafner TUK <hamburge_at_physik.uni-kl.de>
Sent: Sunday, October 25, 2020 5:13 AM
To: McGuire, Kelly <mcg05004_at_byui.edu>; VMD Mailing LIst <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: PBC Wrapping

Hi Kelly,

now I see the issue here.

yeah, it might be impossible to get them all properly wrapped back as they are not connected to each other and for me it looks the same that box seems is too small.

But it may still work, try something like:

* qwrap center "protein and segname PROB" sel "all"

(trying to center and wrap around one specific fragment )

* qwrap center "protein" sel "all"

(use the geom center of the protein as a center and wrap all of them)

Cheers

Ren

On 10/24/2020 3:50 AM, McGuire, Kelly wrote:
The pictures are described in the original post.

What commands would you use to get this protein back together and re-centered?

Also, should the same command(s) work throughout the entire 2 microseconds (if I open all dcds at once), or will it take different commands depending on which segment is leaving the box at different times in the trajectory?

Dr. Kelly L. McGuire

PhD Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

On 10/23/2020 11:15 AM, Ren Hafner TUK wrote:

Sure just send me any Cloud link and I can have a look at the pictures (or via email only to me if the image sizes are not too big.)

I don't know about your available computing resources but from my experiences a Cluster generally has a few nodes with 1TB of RAM which would be enough. I'd try it there.

Give the qwrap tool a try! :)

On 10/23/2020 10:33 AM, McGuire, Kelly wrote:
Thanks for the response! Each DCD is about 10 GB. So, 500 GB for the whole trajectory.

Haven't ever tried qwrap. I thought it was mostly for orthorhombic water box shapes. Maybe it's worth a try.

I couldn't attach the pictures to the first email. Is there a way I can send them to you for better context of the description in my email? It might clarify the problem a bit more. 2-3 of the segments are hanging outside of the water box on one side and the 4th segment is hanging outside the water box on the other side. Can't seem to get all segments back together in the center of the box no matter what set of commands I use....

Dr. Kelly L. McGuire

PhD Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Ren Hafner TUK <hamburge_at_physik.uni-kl.de><mailto:hamburge_at_physik.uni-kl.de>
Sent: Friday, October 23, 2020 2:25 AM
To: McGuire, Kelly <mcg05004_at_byui.edu><mailto:mcg05004_at_byui.edu>; VMD Mailing LIst <vmd-l_at_ks.uiuc.edu><mailto:vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: PBC Wrapping

Dear Kelly,

First recommendation:
    Use Jrme Hnin qwrap tool for wrapping/unwrapping of trajectories.

    https://github.com/jhenin/qwrap-rNFL2SFSMwdf39eCuHPWfd-yTbzQjhLZzLBek&e=>

It is a lot faster than the pbctools wrap command. (:

2. What file sizes are we talking about here? Dozens of GB or TB?

>From my point of view:

    If you have a PC or cluster node with enough RAM it might be better to load the whole 2s DCD at once.

I'd say if the simulation ran properly regarding the Box size (NVT I guess) there shouldn't be too much of a problem regarding wrapping the trajectory. It might just be that the dynamics are unreasonable if the protein segment interact with other parts of themselves by PBC and therefore may invalidate the results.

Kind regards

Ren

On 10/22/2020 11:06 PM, McGuire, Kelly wrote: